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comparison fisherBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children b28e0cfa7ba1
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_fisher" name="bedtools FisherBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1">
2 <description>calculate Fisher statistic between two feature files</description> 2 <description>calculate Fisher statistic between two feature files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools fisher
10 bedtools fisher 10 $strand
11 $strand 11 $split
12 $split 12 -a '$inputA'
13 -a '$inputA' 13 -b '$inputB'
14 -b '$inputB' 14 @OVERLAP@
15 -f $overlap 15 -g @GENOME_FILE@
16 -g @GENOME_FILE@ 16 $reciprocal
17 $reciprocal 17 $m
18 $m 18 > '$output'
19 > '$output' 19 ]]></command>
20 ]]>
21 </command>
22 <inputs> 20 <inputs>
23 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 21 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
24 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 22 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
25 <expand macro="input_conditional_genome_file" /> 23 <expand macro="input_conditional_genome_file" />
26 <expand macro="strand2" /> 24 <expand macro="strand2" />
27 <expand macro="split" /> 25 <expand macro="split" />
28 <expand macro="overlap" /> 26 <expand macro="overlap" />
29 <expand macro="reciprocal" /> 27 <expand macro="reciprocal" />
30 <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue="" 28 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false"
31 label="Merge overlapping intervals before looking at overlap" help="(-m)" /> 29 label="Merge overlapping intervals before looking at overlap" />
32 </inputs> 30 </inputs>
33 <outputs> 31 <outputs>
34 <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/> 32 <data name="output" format_source="inputA" metadata_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
35 </outputs> 33 </outputs>
36 <tests> 34 <tests>
37 <test> 35 <test>
38 <param name="inputA" value="fisherBed1.bed" ftype="bed" /> 36 <param name="inputA" value="fisherBed1.bed" ftype="bed" />
39 <param name="inputB" value="fisherBed2.bed" ftype="bed" /> 37 <param name="inputB" value="fisherBed2.bed" ftype="bed" />
40 <param name="genome_file_opts_selector" value="hist" /> 38 <param name="genome_file_opts_selector" value="hist" />
41 <param name="genome" value="fisherBed.len" ftype="tabular" /> 39 <param name="genome" value="fisherBed.len" ftype="tabular" />
42 <output name="output" file="fisherBed_result1.bed" ftype="bed" /> 40 <output name="output" file="fisherBed_result1.bed" ftype="bed" />
43 </test> 41 </test>
44 </tests> 42 </tests>
45 <help> 43 <help><![CDATA[
46 <![CDATA[
47 **What it does** 44 **What it does**
48 45
49 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files. 46 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
50 47
51 @REFERENCES@ 48 @REFERENCES@
52 ]]> 49 ]]></help>
53 </help>
54 <expand macro="citations" /> 50 <expand macro="citations" />
55 </tool> 51 </tool>